Systems analysis of cell type differentiation in xenopus development

描述(申请人提供)：我们建议提出一个系统生物学框架，用于综合理解早期脊椎动物胚胎发育中导致主要外胚层、中胚层和内胚层细胞类型的信号和转录事件，使用非洲爪哇模式系统。BMP、Nodal和Wnt三条信号通路的受控操纵将被用来驱动多能胚胎细胞朝着不同明确的发育方向发展。我们将描述每一种终点细胞类型和许多中间体，逐步分析细胞做出命运选择时蛋白质和信使核糖核酸水平的变化。我们的团队是由两位专家胚胎学家/细胞生物学家(Kirschner和Gerhart)与一位系统分析和统计推断专家(Peshkin)和一位蛋白质组质谱专家(Gygi)密切合作组成的。我们最近开发的方法将使我们能够达到前所未有的水平，对蛋白质、蛋白质翻译后修饰和mRNA转录本进行检测和量化。在某些情况下，非洲爪哇巨大的卵子和胚胎也可以进行单细胞研究。我们假设，对早期发育的高质量蛋白质组学分析将产生对发育信号通路的新的关键见解。我们的数据集将提供前所未有的系统水平的知识，关于蛋白质在脊椎动物早期发育中的定位和随时间变化的作用，在注定要成为不同细胞类型的细胞中。这一信息对于许多生物学问题将是新的，对胚胎学来说将是革命性的。我们的一套方法将允许快速分析发育信号对关键途径的影响，以及对脊椎动物胚胎发育的总体影响。这些关键途径在以后的发育过程、儿童发育、成人的组织和细胞更新以及以干细胞生物学为基础的再生医学方法中也很重要。它们在很大程度上也是跨物种保守的，有望从模型系统快速转移到人类患者身上。我们希望这些数据将以新的方式了解人类胚胎和儿童中的可遗传缺陷。 公共卫生相关性：我们将应用和开发现代基因组工具，重点研究脊椎动物胚胎中细胞类型的胚胎发育，目标是了解并最终控制细胞分化的途径。这类研究可以促进制定指导细胞分化的程序，最终有助于再生医学在治疗重要人类疾病方面的作用。

DESCRIPTION (provided by applicant): We propose to advance a systems biology framework for an integrative understanding of the signaling and transcriptional events in early vertebrate embryonic development leading to major ectodermal, mesodermal, and endodermal cell types, using the Xenopus laevis model system. Controlled manipulation of three signaling pathways, Bmp, Nodal, and Wnt, will be used to drive multipotent embryonic cells in different well-defined developmental directions. We will characterize each of the endpoint cell types and many intermediates, providing a step- by-step analysis of the changes in protein and mRNA levels as a cell makes fate choices. Our team is a close collaboration between two expert embryologists/cell biologists (Kirschner and Gerhart) with an expert in systematic analysis and statistical inference (Peshkin) and an expert in proteomic mass spectrometry (Gygi). Our recently developed methods will allow us to reach unprecedented levels of detection and quantification of proteins, protein post-translational modifications, and mRNA transcripts. The large size of Xenopus eggs and embryos will also permit single-cell studies in some cases. We hypothesize that high quality proteomic profiling of early development will produce new key insights into developmental signaling pathways. Our dataset will provide an unprecedented degree of systems-level knowledge on the localization- and time-dependent actions of proteins in early vertebrate development, in cells fated to become different cell types. This information will be new for many biological problems, and revolutionary for embryology. Our suite of methods will allow rapid profiling of the effect of developmental signals on key pathways, and on vertebrate embryonic development in general. These key pathways are also important in later developmental processes, in childhood development, tissue and cell turnover in adults, and in approaches to regenerative medicine based on stem cell biology. They are also largely conserved across species, promising rapid transfer from the model system to human patients. We expect that these data will inform on heritable defects in human embryos and children in new ways. PUBLIC HEALTH RELEVANCE: We will apply and develop modern genomic tools focused the embryonic development of cell types in the vertebrate embryo with the goal of understanding and ultimately controlling pathways for cell differentiation. Such studies could facilitate the development of procedures to direct cell differentiation in ways that would ultimately contribute to regenerative medicine in the treatment of important human diseases.